flextaxd

Flexible Taxonomy Databases (FlexTaxD)

FlexTaxD is a versatile tool for the customization and integration of taxonomic classifications from diverse sources. It facilitates the creation, modification, and export of taxonomy databases for bioinformatics applications.

Key Features

• Supported Taxonomy Formats: NCBI, TSV, MP-style (GTDB, QIIME, SILVA, CanSNPer).
• Database Build Programs: Compatible with kraken2, ganon, krakenuniq, and centrifuge.
• Database Customization: Modify, annotate, and clean up taxonomy databases to fit specific research needs.
• Output: Export databases to NCBI formatted files or tab-separated values, with customizable options.
• Data Management: Utilizes a SQLite database to manage data efficiently.

Quick Start

For a complete walkthrough, refer to the FlexTaxD Wiki.

Installation

# With conda using mamba
conda install mamba -n base -c conda-forge
mamba create -c conda-forge -c bioconda -n flextaxd flextaxd

# Manual Python installation
git clone https://github.com/FOI-Bioinformatics/flextaxd
cd flextaxd
pip install .

Usage Examples

# Create a custom taxonomy database
flextaxd --taxonomy_file taxonomy.tsv --database .ftd

# Export database to NCBI format
flextaxd --dump

# Print database statistics
flextaxd --stats

# Get help
flextaxd --help

Taxonomy dumps and the format a program reads

# Export the database in the layout kraken2/krakenuniq read
flextaxd --dump --dbprogram kraken2

# Minimal, tab separated export (no program will read this one)
flextaxd --dump_mini

kraken2 and krakenuniq take the name of a taxid from the trailing columns of names.dmp, and the rank from the trailing columns of nodes.dmp. --dump --dbprogram kraken2 writes those columns; --dump_mini writes a short tab separated file without them, which is meant for reading by a person or another tool. The two are never combined: --dump_mini --dbprogram kraken2 (and an NCBI type dump for a program) stops with an error instead of writing a dump that leaves the built database listing every taxid without a name.

Requirements

• Python >=3.6
• Additional dependencies vary based on executed functions (e.g., ncbi-genome-download for genome downloads).

Visualization Dependencies

• biopython: Required for Newick visualizations.
• matplotlib: For tree visualizations.
• inquirer: For interactive prompts when multiple parents are present.

Database Creation Dependencies

• kraken2, krakenuniq, ganon, centrifuge: Required if create_database is used.

Contributing

Your contributions are welcome! Please refer to the Contribution Guide for details on how to submit pull requests, report issues, or request features.

License

FlexTaxD is open-sourced under the MIT license.

Citation

FlexTaxD is published in Bioinformatics.

Sundell, D. et al. (2021) ‘FlexTaxD: flexible modification of taxonomy databases for improved sequence classification’, Bioinformatics. Edited by J. Kelso. Bioinformatics. doi: 10.1093/bioinformatics/btab621.